Delete command#4
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Two functions with the same name returned different paths (meta index vs semantic index). Renamed for clarity: storage version → getMetaIndexPath, embeddings → getSemanticIndexPath.
MCP inline parsing was missing toLowerCase(), causing tags to be stored with inconsistent casing vs CLI. Now uses shared parseTags() from core.
Creates src/core/operations/delete.ts following the established operation pattern. Handles validation, existence check, bidirectional related-thread reference cleanup (fixes stale references bug), thread file deletion, and non-fatal semantic index cleanup. Returns detailed DeleteResult stats.
Exposes thread deletion as an MCP tool. Calls the deleteThread core operation and returns a summary of what was cleaned up (snippets, file links, related threads, semantic entries). Description explicitly marks the operation as permanent and irreversible.
Replaces direct storage calls and inline semantic cleanup with a single call to deleteThread(). CLI now only handles confirmation prompting and output formatting. Gets related-thread cleanup for free from the operation.
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